Targeted Protein Detection Using an All-in-One Mass Spectrometry

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Targeted Protein Detection using an All-In-One Mass Spectrometry Cartridge Chengsen Zhang, Trevor G Glaros, and Nicholas E Manicke J. Am. Chem. Soc., Just Accepted Manuscript • DOI: 10.1021/jacs.7b05571 • Publication Date (Web): 31 Jul 2017 Downloaded from http://pubs.acs.org on July 31, 2017

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Journal of the American Chemical Society

Targeted Protein Detection using an All-In-One Mass Spectrometry Cartridge Chengsen Zhang,† Trevor Glaros,‡ and Nicholas E Manicke*,† †

Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA ‡ BioSciences Division, BioDefense Branch, US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA

Supporting Information Placeholder

cates detection of PTMs and sequence variants. Development of a simple MS assay capable of resolving proteoforms would have a significant impact on protein detection, including clinical testing. We previously reported simple, single-use MS cartridges for the analysis of drugs which integrated sample preparation, sample storage as a dried spot, and analyte ionization via paper spray, in which paper is used as an inexpensive solid support for extraction, fluid transport, and electrospray ionization.8-9 Here, we describe the development of a mass spectrometry cartridge designed for targeted detection of proteins from complex biofluids such as plasma. Selective enrichment of protein targets is performed oncartridge passively by capillary action and gravity with no pumping. Detection of the intact protein targets then proceeds via ionization of the protein target using a built-in spray substrate consisting of carbon-nanotube (CNT) coated porous polyethylene. The distinguishing feature of this approach is its simplicity and low cost, in effect a combination of inexpensive lateral flow assays with mass spectrometry. Three applications of this cartridge are described for clinically significant problems: 1) identification of T45S variant of apolipoprotein c1, a polymorphism associated with body mass index and obesity, 2) relative quantitation of hemoglobin (Hb) A1C, a marker of diabetes, and 3) identification of sequence variants of transthyretin, which are markers of transthyretin-related hereditary amyloidosis. A 3D printed cartridge (Figure 1) was developed to perform the entire analyte preconcentration and ionization process. An absorbent waste pad in the base of the cartridge draws the sample through the antibody column, which consisted of a plastic tube packed with glass fiber membranes coated with latex bead-antibodies conjugates. All parts were assembled together, and the column holder was slid along the groove between lid and base to switch the position of the antibody column from above

ABSTRACT: We developed a simple 3D printed car-

tridge for mass spectrometry (MS) targeted detection of plasma proteins, including post-translational modifications (PTMS). The cartridge uses an integrated antibody enrichment column to preconcentration the protein target as well as a novel built-in substrate to ionize the protein targets for MS detection. We show several examples of using this cartridge to perform rapid detection of clinically significant proteoforms from plasma samples.

Protein molecules and targets are measured in clinical diagnostic laboratories as tumor markers, acute or chronic disease markers, risk or prognostic markers, and hormones. Immunoassays have been successfully used for decades to detect protein analytes in clinical laboratories, but there remain limitations of this approach. Monoclonal antibodies are expensive to develop and manufacture. Moreover, there are well recognized analytical limitations; for example, most immunoassays do not distinguish between the various proteoforms and variants of a protein present in clinical samples.1 Targeted enrichment of proteins followed by MS detection is a widely used approach to detect different proteoforms. Enrichment is generally performed using antibodies because of their ability to selectively enrich target proteins from protein rich matrices such as plasma. Mass spectrometric immunoassay (MSIA) uses antibody coated beads packed into a pipette tip2 followed by detection of intact proteins by MALDI-MS. Another approach is antibody modification of the MALDI target.3-5 In SISCAPA (stable isotope standards and capture by antipeptide antibodies) and immuno-MALDI, enrichment is performed at the peptide level after digestion.6-7 Peptide level enrichment gives better quantitation and improved sensitivity. However, limited sequence coverage compli-

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the waste pad, where the sample addition and washing steps occurred, to above the spray substrate where ionization by substrate supported electrospray ionization occurred. MS detection was performed on a quadrupole-orbitrap mass spectrometer in full scan mode.

3). The size of the Taylor cone correlates with droplet size, and smaller electrospray droplets correlate with better ionization efficiency.16 The improved protein detection from the CNT-coated PE substrate therefore may arise from balancing the surface energy of the substrate with that of the solvent to generate smaller droplets and more efficient ionization. The substrate must be sufficiently wettable to allow wicking by a polar solvent, necessary to drive fluid and analyte transport, but not so wettable that the Taylor cone is large. The CNT-PE substrate was also found to retain less protein than paper, but the difference was small compared to the improvement in detection limits (supplementary material).

Figure 1. Schematic diagram and photograph of the antibody cartridge. The inserted photograph shows the assembled cartridge in the sample loading/wash. The antibody column extracted target protein from the plasma and a CNT-coated porous polyethylene spray tip was used for substrate supported electrospray.

Figure 2. Full MS spectra obtained by ionizing 10 µg/mL cytochrome c using paper spray (a) and the CNT-coated PE substrate (b). Spectra for two other proteins are in supplementary figure S2.

To achieve selective and sensitive detection of target proteins from biofluids, we utilized an antibody column integrated into the cartridge. In this method, protein preconcentration was performed using a membrane containing latex bead-antibody conjugates. The plasma sample was added to the antibody column where it flowed through by a combination of capillary action and gravity. Excess sample was absorbed into a built-in waste pad in the bottom cartridge, while the target protein was retained on the latex bead conjugates. A washing step was performed by subsequently adding water to the preconcentration column, where it wicked into the waste pad. The protein analyte was then detected by sliding the antibody column to the elution position above the spray substrate and adding 1:1 methanol:water with 2% acetic acid, which acted as both the extraction solution and the spray solvent. Over 90% of captured protein was eluted in the case of cytochrome C (supplemental material).

A number of reports describe the use of paper spray MS for the detection of drugs and other small molecules from blood.10-11 The detection efficiency of proteins by paper spray is relatively poor, however. A paper spray based immunoassay was reported in which a charged probe released from the bound antibody was detected by MS.12 Although this approach has better sensitivity because a small molecule is used for detection, the selectivity is ultimately limited by the antibody. Detection of the probe cannot give any information on the antigen such as PTMs. Improved protein ionization has been reported using paper coated with CNT13 as well as size exclusion membranes.14 Carbon nanotube coated paper has also been utilized for low voltage paper spray.15 We investigated CNT treated paper and as well as a novel substrate, CNT treated porous polyethylene (PE). Photographs and scanning electron microscope images of the spray substrates are shown in Figure S1. Detection limits of the three proteins were improved by coating or dispersing chromatography paper with single-walled CNT (Table S1). The CNT-coated PE even further improved protein detection; CNT-coated PE detection limits were between 10 and 100 times lower compared to the best obtained using CNT treated paper. Detection limits of the protein standards were improved by a factor of 501000 compared to typical paper spray. Mass spectra obtained using paper and CNT-coated PE for three standard protein solutions are shown in Figure 2. The Taylor cone generated from the CNT-coated PE tip was significantly smaller compared to paper (Figure

Figure 3. Taylor cone generated from CNT-PE and paper. The diameter of the Taylor cone generated from the sharp point of CNT-PE was much smaller compared with paper. CNT-coated paper is pictured in supplementary figure S3.

We used polyclonal antibodies as opposed to mono-


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clonal antibodies. While monoclonal antibodies are generally preferred in immunoassays because of their higher selectivity, polyclonal antibodies have a number of advantages for this application. Polyclonal antibodies have higher affinity compared to monoclonal antibodies, they bind to multiple different epitopes which minimizes the risk that a particular proteoform or variant will not bind, and they are cheaper than monoclonal antibodies. The lower selectivity of polyclonal antibodies is not a factor in this application because of the use of MS detection. This approach does necessitate that antibodies against the target protein be available. Antibodies are also the most expensive component of the cartridge. However, use of antibodies in this cartridge are still significantly cheaper with faster development times than traditional immunoassays. Because MS detection is used, high selectivity monoclonal antibodies are not required, which decreases the cost and time associated with antibody generation.

that some of plasma came from individuals with the ApoC1 S45 allele (figure 4b). The protein cartridge was also used to analyze plasma from a single donor; the mass spectrum indicates that the individual donor did not have this allele (figure 4c). In comparison with calculated accurate masses, mass error for detected T45S variant was 0.0056 Da. These results indicate the method has good potential for rapid detection of the ApoC1 T45S variant.

Figure 5. Antibody cartridge analysis of human plasma hemoglobin (Hb). (a) full MS spectrum shows the Hb /β-chain ions with charge state from +11 to +20. SIM spectra (m/z scan window 1.2 Da) show the relative intensities of non-glycated (b) and glycated (c) Hb.

Glycated hemoglobin is a stable minor Hb variant formed in vivo by the non-enzymatic, covalent attachment of glucose. Relative quantitation of a particular Hb fraction, HbA1c, has been used as a marker of glycemia control in diabetes for decades.18 As shown in Figure 5, several hemoglobin species were identified using the protein detection cartridge, such as nonglycated -/βchains (Figure 5a), and glycated -/β-chains (Figure 5a insert spectrum). The Hb and glycated Hb were monitored using single ion monitoring (SIM) of the +15 charge state as shown in figure 5b and 5c. The mass error for the detected non-glycated Hb β-chain and glycated Hb β-chain were 0.012 Da and -0.079 Da, respectively. The relative intensity of glycated Hb was ~7% compared to unglycated Hb, which is similar to the expected proportion.19-20 The results indicate the method has potential for relative quantitation of Hb and HbA1c. Transthyretin (TTR) is a 55kDa homotetramer protein that transports thyroxine and retinol in blood and cerebrospinal fluid. Misfolding and aggregation of wild-type (wt) and mutant transthyretin protein (TTR) is the cause

Figure 4. The MS protein detection cartridge analysis of human plasma apolipoprotein c1 (ApoC1). (a) full MS spectrum obtained from the pooled human plasma sample showing the ApoC1 full-length, truncated, and truncated T45S variant. Narrower MS scan range shows the truncated ApoC1 +6 ions obtained from (b) pooled human plasma and (c) individual donated plasma.

We investigated three clinically significant applications of the MS protein detection cartridge. Apolipoprotein C1 (ApoC1) T45S variant is a naturally occurring amino acid polymorphism that has been associated with elevated body mass index and diabetes.17 As shown in Figure 4a, three ApoC1 species were identified in the MS spectrum obtained from a pooled human plasma sample, including full-length ApoC1 (6.6 kDa), truncated ApoC1(minus amino-terminal Thr-Pro, 6.4 kDa), and truncated T45S variant (∆m= -14.03 Da). Detection of the T45S variant in the pooled plasma sample indicated



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of transthyretin amyloidosis (ATTR), a severe and fatal disease characterized by abnormal deposits of TTR amyloids. Mass spectrometry is used to screen for ATTR.20 The antibody cartridge was successfully used to detect wt TTR as well as various TTR mutants from human plasma samples. Supplementary Figure S4 shows the mass spectrum obtained for the +10 charge state of wt TTR. The unmodified TTR was a relatively minor component; the cysteine, glutathione, and sulfonate PTMs were all more intense. To reduce the complexity of the mass spectrum, we spiked the reducing agent Tris(2carboxyethyl)phosphine hydrochloride (TCEP-HCl). This procedure, performed on-cartridge in the extraction/spray solvent without a separate step, succeeding in eliminating the S-cysteine and S-glutathione modifications (Figure S4), although the S-sulfonation remained. Four different TTR mutants in six ATTR clinical samples were clearly identified and differentiated from wt TTR. Figure 6 shows the charge-state deconvoluted mass spectra obtained from a wt sample and a representative ATTR sample. The spectrum from the ATTR sample indicates the patient is heterozygous for wild type TTR and a TTR variant with a ∆m of 32.06 Da. This mass shift is consistent with substitution of valine30 for methionine, the most common mutation found in TTR associated neuropathy.22

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cartridge better enables MS-based detection of protein targets, which is important in clinical diagnostics and other fields. While MS is expensive relative to traditional immunoassay detection methods, mass spectrometry is better suited for distinguishing post-translational modifications, sequence variants, and other proteoforms. ASSOCIATED CONTENT Supporting Information.

The Supporting Information is available free of charge on the ACS Publications website. Materials, full experimental details, supplemental figures S1-S4 and supplemental table S1 (PDF)

AUTHOR INFORMATION Corresponding Author

*E-mail: [email protected] Notes

The authors declare no competing financial interest.

ACKNOWLEDGMENT The authors acknowledge Thermo Scientific for funding and other supporting. We also thank Merrill Benson MD, IU School of Medicine, for supplying the ATTR samples. REFERENCES (1) Anderson, N. L. Clin. Chem. 2010, 56, 177. (2) Nelson, R. W.; Krone, J. R.; Bieber, A. L.; Williams, P. Anal. Chem. 1995, 67, 1153. (3) Liang, X. L.; Lubman, D. M.; Rossi, D. T.; Nordblom, G. D.; Barksdale, C. M. Anal. Chem. 1998, 70, 498. (4) Min, D. H.; Su, J.; Mrksich, M. Angew. Chem., Int. Ed. 2004, 43, 5973. (5) Pompach, P.; Novakova, J.; Kavan, D.; Benada, O.; Ruzicka, V.; Volny, M.; Novak, P. Clin. Chem. 2016, 62, 270. (6) Anderson, N. L.; Anderson, N. G.; Haines, L. R.; Hardie, D. B.; Olafson, R. W.; Pearson, T. W. J. Proteome Res. 2004, 3, 235. (7) Warren, E. N.; Elms, P. J.; Parker, C. E.; Borchers, C. H. Anal. Chem. 2004, 76, 4082. (8) Zhang, C.; Manicke, N. E. Anal. Chem. 2015, 87, 6212. (9) Bills, B. J.; Manicke, N. E. Clin. Mass Spectrom. 2016, 2, 18. (10) Wang, H.; Liu, J.; Cooks, R. G.; Ouyang, Z. Angew. Chem., Int. Ed. 2010, 49, 877. (11) Manicke, N. E.; Bills, B. J.; Zhang, C. Bioanalysis 2016, 8, 589. (12) Chen, S.; Wan, Q.; Badu-Tawiah, A. K. J. Am. Chem. Soc. 2016, 138, 6356. (13) Han, F.; Yang, Y.; Ouyang, J.; Na, N. Analyst 2015, 140, 710. (14) Zhang, M.; Lin, F. K.; Xu, J. G.; Xu, W. Anal. Chem. 2015, 87, 3123. (15) Narayanan, R.; Sarkar, D.; Cooks, R. G.; Pradeep, T. Angew. Chem., Int. Ed. 2014, 53, 5936. (16) Juraschek, R.; Dulcks, T.; Karas, M. J. Am. Soc. Mass Spectrom. 1999, 10, 300. (17) Kasthuri, R. S.; McMillan, K. R.; Flood-Urdangarin, C.; Harvey, S. B.; Wilson-Grady, J. T.; Nelsestuen, G. L. Int. J. Obes. (Lond) 2007, 31, 1334. (18) Gillery, P. Clin. Chem. Lab. Med. 2013, 51, 65. (19) Weykamp, C. Ann. Lab. Med. 2013, 33, 393. (20) Lim, A.; Prokaeva, T.; McComb, M. E.; O'Connor, P. B.; Théberge, R.; Connors, L. H.; Skinner, M.; Costello, C. E. Anal. Chem. 2002, 74, 741. (21) Saraiva, M. J. M. J. Peripher. Nerv. Syst. 1996, 1, 179.

Figure 6. The charge-state deconvoluted MS spectra obtained by antibody cartridge analysis of human plasma from a wt sample (a) and a ATTR plasma sample (b). Only wild type TTR, including free thiol wt-TTR and Ssulfonation wt-TTR, can be detected from normal sample, while a mutant TTR with ∆m=32.0 Da was identified from the ATTR sample.

In summary, we describe a simple, all-in-one 3D printed cartridge which enables targeted protein detection from plasma samples by mass spectrometry. The unique feature of this device is that both protein enrichment as well as ionization occur from one device. Because of the simplicity of the analytical procedure, this


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Targeted Protein Detection Using an All-in-One Mass Spectrometry

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